Re: [R-sig-phylo] Will phyloXML in R be useful?
Hi Hilmar, That sounds good. I've actually managed to build rphyloxml very quickly for creating phyloXML files from phylo (ape) objects. https://uscbiostats.github.io/rphyloxml/ Perhaps we should continue this discussion outside of the list to see how can we integrate both packages (no need to have rphyloxml as a package aside, happy to join RNeXML :)) Best, George G. Vega Yon +1 (626) 381 8171 http://ggvy.cl On Thu, Dec 14, 2017 at 4:22 PM, Hilmar Lapp wrote: > Hi George, > > Yes, there’s RNeXML. Glad you found it on your own, I’ve been occupied > with a workshop. Note that there’s a publication on RNeXML too, as you’ve > probably seen in the README on Github. > > Personally, I think it’d be great to have phyloXML support as well in the > R ecosystem. However, I’d argue that while the two exchange standards have > different strengths (and NeXML is not without its own “warts”), for the > benefit of the user (typically a biology scientist-developer) it would seem > to be vastly preferable if these standards converge at the R API level. So > maybe phyloXML support could be added on to RNeXML, or if its own package, > at least the R API signature could be kept in synchrony? > > -hilmar > > > On Dec 14, 2017, at 3:41 PM, George Vega Yon > wrote: > > > > Hey, > > > > Just for the record. I just found two alternatives that seem to be in > > active development, nexml (www.nexml.org) and RecPhyloXML ( > > https://urldefense.proofpoint.com/v2/url?u=http-3A__ > phylariane.univ-2Dlyon1.fr_recphyloxml_&d=DwIGaQ&c= > imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_ > 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu- > 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=5CdlhUFqJAcw9qGduCmWrGXPwhWFUh > ZMcOss0uysZ34&e= ). nexml is supported by > > rOpenSci (https://urldefense.proofpoint.com/v2/url?u=https- > 3A__github.com_ropensci_RNeXML&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y > HLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_ > Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=E2KdcumsPG- > JacTs6EbDx9PNds1g15J0lpbZVFgcnLs&e= ), and both have C++/phython > > APIs that can be useful for R package development. > > > > I still may try to get something done on PhyloXML since jsPhyloSVG, which > > I'm working on now https://urldefense.proofpoint.com/v2/url?u=https-3A__ > uscbiostats.github.io_jsPhyloSVG_&d=DwIGaQ&c= > imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_ > 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu- > 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=qCOKU5kc59kVmuDmY13hm0h_F0- > 5VtB-8YC5dp3Nc_I&e= , only supports > > annotations in PhyloXML (it does support nexml trees, but I don't think > it > > support annotations). > > > > Best, > > > > George G. Vega Yon > > +1 (626) 381 8171 <(626)%20381-8171> > > https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&d=DwIGaQ&c= > imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_ > 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu- > 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3- > LJHbo4BTkG73yMtknFw&e= > > > > On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon > > wrote: > > > >> That's a good suggestion. I'll reach out the rOpenSci people/ > >> > >> Still, I'm starting a repo here: https://urldefense.proofpoint. > com/v2/url?u=https-3A__github.com_USCBiostats_rphyloxml&d=DwIGaQ&c= > imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_ > 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu- > 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv- > IATJ8VuI&e= > >> will start dropping stuff there. > >> > >> Best, > >> > >> George G. Vega Yon > >> +1 (626) 381 8171 <(626)%20381-8171> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&d=DwIGaQ&c= > imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_ > 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu- > 6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3- > LJHbo4BTkG73yMtknFw&e= > >> > >> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop > >> wrote: > >> > >>> Sounds like a good idea. Not sure if you’re reinventing the wheel or > not. > >>> Sounds like something ROpenSci might support; see: > >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > com_ropensci_onboarding&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y > HLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_ > Y&m=izAgipXSIMSu-6nAHEQ
Re: [R-sig-phylo] Will phyloXML in R be useful?
Hey, Just for the record. I just found two alternatives that seem to be in active development, nexml (www.nexml.org) and RecPhyloXML ( http://phylariane.univ-lyon1.fr/recphyloxml/). nexml is supported by rOpenSci (https://github.com/ropensci/RNeXML), and both have C++/phython APIs that can be useful for R package development. I still may try to get something done on PhyloXML since jsPhyloSVG, which I'm working on now https://uscbiostats.github.io/jsPhyloSVG/, only supports annotations in PhyloXML (it does support nexml trees, but I don't think it support annotations). Best, George G. Vega Yon +1 (626) 381 8171 <(626)%20381-8171> http://ggvy.cl On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon wrote: > That's a good suggestion. I'll reach out the rOpenSci people/ > > Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml > will start dropping stuff there. > > Best, > > George G. Vega Yon > +1 (626) 381 8171 <(626)%20381-8171> > http://ggvy.cl > > On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop > wrote: > >> Sounds like a good idea. Not sure if you’re reinventing the wheel or not. >> Sounds like something ROpenSci might support; see: >> https://github.com/ropensci/onboarding >> >> >> >> >> From: George Vega Yon >> Reply: George Vega Yon >> Date: December 12, 2017 at 4:13:59 PM >> To: Group R-sig-phylo >> >> Subject: [R-sig-phylo] Will phyloXML in R be useful? >> >> Hey, >> >> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library >> for visualizing phylogenetic trees on the web browser) in R, and just got >> to learn about the phyloXML format. Googling around and checking out this >> email list archives it seems that there's no support for this format in >> R. >> >> My question is: how useful do you think having this in R will be? I'm >> willing to write an R package to read/write trees in this format (done >> before with GEXF, which is for networks in general). But I just want to >> make sure that (1) this will be useful for the community, and (2) I'm not >> reinventing the wheel (is anybody working on this now?). What are your >> thoughts? >> >> Best, >> >> George G. Vega Yon >> +1 (626) 381 8171 <(626)%20381-8171> >> http://ggvy.cl >> >> [[alternative HTML version deleted]] >> >> ___ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Will phyloXML in R be useful?
That's a good suggestion. I'll reach out the rOpenSci people/ Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml will start dropping stuff there. Best, George G. Vega Yon +1 (626) 381 8171 http://ggvy.cl On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop wrote: > Sounds like a good idea. Not sure if you’re reinventing the wheel or not. > Sounds like something ROpenSci might support; see: > https://github.com/ropensci/onboarding > > > > > From: George Vega Yon > Reply: George Vega Yon > Date: December 12, 2017 at 4:13:59 PM > To: Group R-sig-phylo > > Subject: [R-sig-phylo] Will phyloXML in R be useful? > > Hey, > > Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library > for visualizing phylogenetic trees on the web browser) in R, and just got > to learn about the phyloXML format. Googling around and checking out this > email list archives it seems that there's no support for this format in R. > > My question is: how useful do you think having this in R will be? I'm > willing to write an R package to read/write trees in this format (done > before with GEXF, which is for networks in general). But I just want to > make sure that (1) this will be useful for the community, and (2) I'm not > reinventing the wheel (is anybody working on this now?). What are your > thoughts? > > Best, > > George G. Vega Yon > +1 (626) 381 8171 <(626)%20381-8171> > http://ggvy.cl > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Will phyloXML in R be useful?
Hey, Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library for visualizing phylogenetic trees on the web browser) in R, and just got to learn about the phyloXML format. Googling around and checking out this email list archives it seems that there's no support for this format in R. My question is: how useful do you think having this in R will be? I'm willing to write an R package to read/write trees in this format (done before with GEXF, which is for networks in general). But I just want to make sure that (1) this will be useful for the community, and (2) I'm not reinventing the wheel (is anybody working on this now?). What are your thoughts? Best, George G. Vega Yon +1 (626) 381 8171 http://ggvy.cl [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Possible Bug in ape::read.tree
Hi Klaus,
Since I'm actually working with the complete PANTHER 11.1 database, I wrote
a short document in our project's website comparing both ape and
rncl reading ~13,000 trees. ape::read.tree does the job and identifies and
reads the singleton as expected. Overall, while I see that the new version
of the read.tree function is significantly faster, it does not seem to be
significantly faster than rncl (both perform pretty good).
You can find the document here:
https://github.com/USCbiostats/aphylo/blob/master/playground/ape_now_supports_singletons.md
Best,
George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon
On Tue, Sep 5, 2017 at 5:55 PM, Klaus Schliep
wrote:
> Dear George & list,
> you can try install the development version of ape, which can handle
> singleton nodes:
> download.packages("ape", ".", repos = "http://ape-package.ird.fr/";)
> and than install the package from source. See
> http://ape-package.ird.fr/ape_installation.html for more details.
> For you tree the new version seems to import tree fine.
> Emmanuel and I are keen to get feedback on the new read.tree() function so
> please give it a try.
> Kind regards,
> Klaus
>
>
>
>
> On Tue, Sep 5, 2017 at 5:37 PM, Liam J. Revell
> wrote:
>
>> Hi George. Mario is correct that phytools can read a tree with singleton
>> nodes (if that is indeed your problem), but the name of the function is
>> read.newick. Good luck! - Liam
>>
>> Liam J. Revell, Associate Professor of Biology
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/liam.revell/
>> email: liam.rev...@umb.edu
>> blog: http://blog.phytools.org
>>
>>
>> On 9/5/2017 4:17 PM, George Vega Yon wrote:
>>
>>> Hi Mario,
>>>
>>> That sounds great!
>>>
>>> Thanks,
>>>
>>> George G. Vega Yon
>>> +1 (626) 381 8171
>>> http://cana.usc.edu/vegayon
>>>
>>> On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo <
>>> mariojm...@gmail.com> wrote:
>>>
>>> Hi, George,
>>>>
>>>> Ape package do not read tree with singletons, yet. New version will
>>>> read.
>>>> You can use readTree from phytools package for while.
>>>>
>>>> Best regards,
>>>>
>>>> Mario
>>>>
>>>>
>>>> On 5 Sep 2017 5:53 p.m., "George Vega Yon" wrote:
>>>>
>>>> Hi,
>>>>
>>>> When trying to read this tree with the ape::read.tree function :
>>>>
>>>> ((AN14:0.000,AN15:0.000):0.000[&&NHX:Ev=0>1:S=
>>>> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&&NHX:Ev=0>
>>>> 1:S=Murinae:ID=AN16]):0.000[&&NHX:Ev=0>1:S=Euarchontoglires:
>>>> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&&NHX:Ev=0>1:S=
>>>> Laurasiatheria:ID=AN19]):0.000[&&NHX:Ev=0>1:S=Eutheria:
>>>> ID=AN11],AN22:0.004):0.003[&&NHX:Ev=0>1:S=Mammalia:ID=AN10]
>>>> ,AN23:0.000):0.014[&&NHX:Ev=0>1:S=Amniota:ID=AN9],AN24:0.
>>>> 017):0.021[&&NHX:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.
>>>> 066,AN28:0.052):0.010[&&NHX:Ev=1>0:ID=AN26],(AN30:0.031,
>>>> AN31:0.014):0.003[&&NHX:Ev=1>0:ID=AN29]):0.021[&&NHX:Ev=0>
>>>> 1:S=Teleostei:ID=AN25]):0.147[&&NHX:Ev=0>1:S=Osteichthyes:
>>>> ID=AN7],AN32:0.194):0.104[&&NHX:Ev=0>1:S=Deuterostomia:ID=
>>>> AN6],((AN35:0.020,AN36:0.038):0.416[&&NHX:Ev=0>1:S=
>>>> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&
>>>> &NHX:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&&NHX:Ev=0>
>>>> 1:S=Arthropoda:ID=AN37]):0.118[&&NHX:Ev=0>1:S=Ecdysozoa:
>>>> ID=AN33],AN42:0.381):0.594[&&NHX:Ev=0>1:S=Bilateria:ID=AN5]
>>>> ,AN43:2.000):0.414[&&NHX:Ev=0>1
>>>> :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&
>>>> &NHX:Ev=0>1:S=
>>>> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&&NHX:Ev=0>
>>>> 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&&
>>>> NHX:Ev=0>1:S=
>>>> Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:
>>>> 0.186):0.143[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:
>>>> 0.331):0.332[&&NHX:Ev=0>1:S=Sordariomycetes-Leotiomycetes:
>>>> ID=AN58]):0.467[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.
>&
Re: [R-sig-phylo] Possible Bug in ape::read.tree
Hi Mario, That sounds great! Thanks, George G. Vega Yon +1 (626) 381 8171 http://cana.usc.edu/vegayon On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Hi, George, > > Ape package do not read tree with singletons, yet. New version will read. > You can use readTree from phytools package for while. > > Best regards, > > Mario > > > On 5 Sep 2017 5:53 p.m., "George Vega Yon" wrote: > > Hi, > > When trying to read this tree with the ape::read.tree function : > > ((AN14:0.000,AN15:0.000):0.000[&&NHX:Ev=0>1:S= > Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&&NHX:Ev=0> > 1:S=Murinae:ID=AN16]):0.000[&&NHX:Ev=0>1:S=Euarchontoglires: > ID=AN12],(AN20:0.000,AN21:0.000):0.000[&&NHX:Ev=0>1:S= > Laurasiatheria:ID=AN19]):0.000[&&NHX:Ev=0>1:S=Eutheria: > ID=AN11],AN22:0.004):0.003[&&NHX:Ev=0>1:S=Mammalia:ID=AN10] > ,AN23:0.000):0.014[&&NHX:Ev=0>1:S=Amniota:ID=AN9],AN24:0. > 017):0.021[&&NHX:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0. > 066,AN28:0.052):0.010[&&NHX:Ev=1>0:ID=AN26],(AN30:0.031, > AN31:0.014):0.003[&&NHX:Ev=1>0:ID=AN29]):0.021[&&NHX:Ev=0> > 1:S=Teleostei:ID=AN25]):0.147[&&NHX:Ev=0>1:S=Osteichthyes: > ID=AN7],AN32:0.194):0.104[&&NHX:Ev=0>1:S=Deuterostomia:ID= > AN6],((AN35:0.020,AN36:0.038):0.416[&&NHX:Ev=0>1:S= > Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[& > &NHX:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&&NHX:Ev=0> > 1:S=Arthropoda:ID=AN37]):0.118[&&NHX:Ev=0>1:S=Ecdysozoa: > ID=AN33],AN42:0.381):0.594[&&NHX:Ev=0>1:S=Bilateria:ID=AN5] > ,AN43:2.000):0.414[&&NHX:Ev=0>1 > :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&&NHX:Ev=0>1:S= > Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&&NHX:Ev=0> > 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&&NHX:Ev=0>1:S= > Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61: > 0.186):0.143[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62: > 0.331):0.332[&&NHX:Ev=0>1:S=Sordariomycetes-Leotiomycetes: > ID=AN58]):0.467[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN56]):0. > 432[&&NHX:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48], > AN63:0.864):0.223[&&NHX:Ev=0>1:S=Ascomycota:ID=AN47],(AN65: > 0.613,AN66:0.930,AN67:0.755):0.332[&&NHX:Ev=0>1:S= > Basidiomycota:ID=AN64]):0.618[&&NHX:Ev=0>1:S=Dikarya:ID= > AN46],((AN74:0.337,AN75:0.406):0.298[&&NHX:Ev=0>1:S= > Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&&NHX:Ev=0> > 1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&&NHX:Ev=0>1:S= > Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83: > 0.403):0.191[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84: > 0.366):0.140[&&NHX:Ev=0>1:S=Sordariomyc > etes-Leotiomycetes:ID=AN80]):0.457[&&NHX:Ev=0>1:S= > Pezizomycotina:ID=AN78]):0.331[&&NHX:Ev=0>1:S=Pezizomycotina- > Saccharomycotina:ID=AN70],AN85:0.737):0.128[&&NHX:Ev=0> > 1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&&NHX: > Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&&NHX:Ev=0>1:S= > Dikarya:ID=AN68]):0.117[&&NHX:Ev=1>0:ID=AN45],(AN90:0.984, > AN91:0.893):0.158[&&NHX:Ev=1>0:ID=AN89]):0.262[&&NHX:Ev=0> > 1:S=Fungi:ID=AN44]):0.394[&&NHX:Ev=0>1:S=Opisthokonts:ID= > AN3],(AN93:0.457,AN94:0.462):0.860[&&NHX:Ev=0>1:S= > Dictyostelium:ID=AN92]):0.301[&&NHX:Ev=0>1:S=Unikonts:ID= > AN2],AN95:1.440,AN96:2.000):2.000[&&NHX:Ev=0>1:S=Eukaryota: > ID=AN1])[&&NHX:Ev=1>0:ID=AN0]; > > I get the following error: "The tree has apparently singleton node(s): > cannot read tree file. Reading Newick file aborted at tree no. 1", > which seems to be wrong since I can actually read this tree without problem > using rncl::read_newick_phylo and this online tool > http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e > 9f&algid=ce443ed1e53858bf4e11d1e069c7a927 > > I understand that this particular tree is a modified version of Newick's > format, but this is the first time that I have problems reading this type > of tree. > > Here my session info: > > > devtools::session_info() > Session info > > - > setting value > version R version 3.4.1 (2017-06-30) > system x86_64, linux-gnu > ui RStudio (1.0.143) > languag
[R-sig-phylo] Possible Bug in ape::read.tree
Hi, When trying to read this tree with the ape::read.tree function : ((AN14:0.000,AN15:0.000):0.000[&&NHX:Ev=0>1:S=Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&&NHX:Ev=0>1:S=Murinae:ID=AN16]):0.000[&&NHX:Ev=0>1:S=Euarchontoglires:ID=AN12],(AN20:0.000,AN21:0.000):0.000[&&NHX:Ev=0>1:S=Laurasiatheria:ID=AN19]):0.000[&&NHX:Ev=0>1:S=Eutheria:ID=AN11],AN22:0.004):0.003[&&NHX:Ev=0>1:S=Mammalia:ID=AN10],AN23:0.000):0.014[&&NHX:Ev=0>1:S=Amniota:ID=AN9],AN24:0.017):0.021[&&NHX:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0.066,AN28:0.052):0.010[&&NHX:Ev=1>0:ID=AN26],(AN30:0.031,AN31:0.014):0.003[&&NHX:Ev=1>0:ID=AN29]):0.021[&&NHX:Ev=0>1:S=Teleostei:ID=AN25]):0.147[&&NHX:Ev=0>1:S=Osteichthyes:ID=AN7],AN32:0.194):0.104[&&NHX:Ev=0>1:S=Deuterostomia:ID=AN6],((AN35:0.020,AN36:0.038):0.416[&&NHX:Ev=0>1:S=Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[&&NHX:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&&NHX:Ev=0>1:S=Arthropoda:ID=AN37]):0.118[&&NHX:Ev=0>1:S=Ecdysozoa:ID=AN33],AN42:0.381):0.594[&&NHX:Ev=0>1:S=Bilateria:ID=AN5],AN43:2.000):0.414[&&NHX:Ev=0>1 :S=Eumetazoa:ID=AN4],AN52:0.484,AN53:0.427):0.418[&&NHX:Ev=0>1:S=Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&&NHX:Ev=0>1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&&NHX:Ev=0>1:S=Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61:0.186):0.143[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62:0.331):0.332[&&NHX:Ev=0>1:S=Sordariomycetes-Leotiomycetes:ID=AN58]):0.467[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN56]):0.432[&&NHX:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48],AN63:0.864):0.223[&&NHX:Ev=0>1:S=Ascomycota:ID=AN47],(AN65:0.613,AN66:0.930,AN67:0.755):0.332[&&NHX:Ev=0>1:S=Basidiomycota:ID=AN64]):0.618[&&NHX:Ev=0>1:S=Dikarya:ID=AN46],((AN74:0.337,AN75:0.406):0.298[&&NHX:Ev=0>1:S=Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&&NHX:Ev=0>1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&&NHX:Ev=0>1:S=Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83:0.403):0.191[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84:0.366):0.140[&&NHX:Ev=0>1:S=Sordariomyc etes-Leotiomycetes:ID=AN80]):0.457[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN78]):0.331[&&NHX:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN70],AN85:0.737):0.128[&&NHX:Ev=0>1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&&NHX:Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&&NHX:Ev=0>1:S=Dikarya:ID=AN68]):0.117[&&NHX:Ev=1>0:ID=AN45],(AN90:0.984,AN91:0.893):0.158[&&NHX:Ev=1>0:ID=AN89]):0.262[&&NHX:Ev=0>1:S=Fungi:ID=AN44]):0.394[&&NHX:Ev=0>1:S=Opisthokonts:ID=AN3],(AN93:0.457,AN94:0.462):0.860[&&NHX:Ev=0>1:S=Dictyostelium:ID=AN92]):0.301[&&NHX:Ev=0>1:S=Unikonts:ID=AN2],AN95:1.440,AN96:2.000):2.000[&&NHX:Ev=0>1:S=Eukaryota:ID=AN1])[&&NHX:Ev=1>0:ID=AN0]; I get the following error: "The tree has apparently singleton node(s): cannot read tree file. Reading Newick file aborted at tree no. 1", which seems to be wrong since I can actually read this tree without problem using rncl::read_newick_phylo and this online tool http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e9f&algid=ce443ed1e53858bf4e11d1e069c7a927 I understand that this particular tree is a modified version of Newick's format, but this is the first time that I have problems reading this type of tree. Here my session info: > devtools::session_info() Session info - setting value version R version 3.4.1 (2017-06-30) system x86_64, linux-gnu ui RStudio (1.0.143) language (EN) collate en_US.UTF-8 tz America/New_York date 2017-09-05 Packages - package * version date source ape 4.1 2017-02-14 CRAN (R 3.4.0) assertthat0.2.0 2017-04-11 CRAN (R 3.4.0) base* 3.4.1 2017-06-30 local compiler 3.4.1 2017-06-30 local datasets* 3.4.1 2017-06-30 local devtools 1.13.3 2017-08-02 CRAN (R 3.4.0) digest0.6.12 2017-01-27 CRAN (R 3.4.0) graphics* 3.4.1 2017-06-30 local grDevices * 3.4.1 2017-06-30 local grid 3.4.1 2017-06-30 local lattice 0.20-35 2017-03-25 CRAN (R 3.4.1) magrittr 1.5 2014-11-22 CRAN (R 3.4.0) memoise 1.1.0 2017-04-21 CRAN (R 3.4.0) methods * 3.4.1 2017-06-30 local nlme 3.1-131 2017-02-06 CRAN (R 3.4.1) parallel 3.4.1 2017-06-30 local prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1) progress 1.1.2 2016-12-14 CRAN (R 3.4.1) R62.2.2 2017-06-17 CRAN (R 3.4.0) Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.0) rncl 0.8.2 2016-12-16 CRAN (R 3.4.1) stats * 3.4.1 2017-06-30 local tools 3.4.1 2017-06-30 local utils * 3.4.1 2017-06-30 local withr 2.0.0 2017-07-28 CRAN (R 3.4.0) Any ideas? Best, George G. Vega Yon +1 (626)
